File: Test2DMeshBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 16722ms, 84.75% of 19732ms total Dropped 793 nodes (cum <= 98.66ms) flat flat% sum% cum cum% 0 0% 0% 19685ms 99.76% __libc_start_call_main 0 0% 0% 19685ms 99.76% __libc_start_main_impl 0 0% 0% 19685ms 99.76% _start 0 0% 0% 19665ms 99.66% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 19665ms 99.66% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 19665ms 99.66% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 19665ms 99.66% main 0 0% 0% 19626ms 99.46% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 19626ms 99.46% CxxTest::TestRunner::runTest (inline) 0 0% 0% 19626ms 99.46% Test2DCryptRepresentativeSimulation::TestRepresentativeSimulationForProfiling 1ms 0.0051% 0.0051% 19599ms 99.33% AbstractCellBasedSimulation::Solve 0 0% 0.0051% 15187ms 76.97% AbstractCellBasedSimulation::UpdateCellPopulation 0 0% 0.0051% 9981ms 50.58% AbstractCellBasedSimulation::DoCellBirth 4ms 0.02% 0.025% 9890ms 50.12% Cell::ReadyToDivide 3ms 0.015% 0.041% 9806ms 49.70% AbstractPhaseBasedCellCycleModel::ReadyToDivide 0 0% 0.041% 9668ms 49.00% AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase 13ms 0.066% 0.11% 9662ms 48.97% AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase 0 0% 0.11% 9649ms 48.90% CellCycleModelOdeHandler::SolveOdeToTime 70ms 0.35% 0.46% 9493ms 48.11% AbstractOneStepIvpOdeSolver::InternalSolve 881ms 4.46% 4.93% 8637ms 43.77% RungeKutta4IvpOdeSolver::CalculateNextYValue 3597ms 18.23% 23.16% 7532ms 38.17% WntCellCycleOdeSystem::EvaluateYDerivatives 2ms 0.01% 23.17% 5097ms 25.83% MeshBasedCellPopulation::Update 84ms 0.43% 23.59% 3991ms 20.23% AbstractCellProperty::IsType (inline) 9ms 0.046% 23.64% 3925ms 19.89% Cylindrical2dMesh::ReMesh 581ms 2.94% 26.58% 2775ms 14.06% AbstractCellProperty::IsSame 0 0% 26.58% 2433ms 12.33% OffLatticeSimulation::UpdateCellLocationsAndTopology 401ms 2.03% 28.61% 2194ms 11.12% std::type_info::operator== (inline) 0 0% 28.61% 2123ms 10.76% MutableMesh::ReMesh 0 0% 28.61% 2101ms 10.65% ForwardEulerNumericalMethod::UpdateAllNodePositions 6ms 0.03% 28.64% 2055ms 10.41% AbstractNumericalMethod::ComputeForcesIncludingDamping 2ms 0.01% 28.65% 1974ms 10.00% AbstractCellPopulation::WriteResultsToFiles 878ms 4.45% 33.10% 1913ms 9.69% std::_Rb_tree::_M_lower_bound (inline) 1726ms 8.75% 41.85% 1726ms 8.75% __strcmp_avx2 161ms 0.82% 42.67% 1689ms 8.56% TetrahedralMesh::EdgeIterator::operator++ 56ms 0.28% 42.95% 1421ms 7.20% std::_Rb_tree::find (inline) 2ms 0.01% 42.96% 1143ms 5.79% MeshBasedCellPopulation::UpdateNodePairs 4ms 0.02% 42.98% 1129ms 5.72% MeshBasedCellPopulationWithGhostNodes::ApplyGhostForces 13ms 0.066% 43.05% 1082ms 5.48% TetrahedralMesh::ImportFromMesher 68ms 0.34% 43.39% 1045ms 5.30% operator new 13ms 0.066% 43.46% 1014ms 5.14% MeshBasedCellPopulation::SpringIterator::operator++ 227ms 1.15% 44.61% 965ms 4.89% __GI___libc_malloc 7ms 0.035% 44.64% 954ms 4.83% std::set::insert (inline) 18ms 0.091% 44.73% 947ms 4.80% std::_Rb_tree::_M_insert_unique 28ms 0.14% 44.88% 908ms 4.60% std::__new_allocator::allocate (inline) 0 0% 44.88% 904ms 4.58% std::allocator_traits::allocate (inline) 0 0% 44.88% 853ms 4.32% std::set::count (inline) 0 0% 44.88% 785ms 3.98% triangulate 7ms 0.035% 44.91% 744ms 3.77% MeshBasedCellPopulationWithGhostNodes::AcceptCellWritersAcrossPopulation 60ms 0.3% 45.22% 728ms 3.69% std::map::operator[] (partial-inline) 0 0% 45.22% 708ms 3.59% delaunay 2ms 0.01% 45.23% 707ms 3.58% divconqdelaunay 0 0% 45.23% 674ms 3.42% AbstractTwoBodyInteractionForce::AddForceContribution 6ms 0.03% 45.26% 661ms 3.35% CellPopulationElementWriter::Visit 382ms 1.94% 47.19% 660ms 3.34% _int_malloc 18ms 0.091% 47.28% 653ms 3.31% std::less::operator() (inline) 648ms 3.28% 50.57% 648ms 3.28% std::_Rb_tree::_S_right (inline) 632ms 3.20% 53.77% 646ms 3.27% WntCellCycleOdeSystem::CalculateStoppingEvent 635ms 3.22% 56.99% 635ms 3.22% std::operator< (inline) 0 0% 56.99% 604ms 3.06% std::_Rb_tree::_M_create_node (inline) 184ms 0.93% 57.92% 602ms 3.05% __dynamic_cast 25ms 0.13% 58.05% 597ms 3.03% std::_Rb_tree::_M_insert_ (inline) 3ms 0.015% 58.06% 596ms 3.02% MeshBasedCellPopulation::AcceptCellWriter 22ms 0.11% 58.17% 590ms 2.99% AbstractVariableSizeTwoBodyInteractionForce::CalculateForceBetweenNodes 0 0% 58.17% 577ms 2.92% std::_Rb_tree::lower_bound (inline) 0 0% 58.17% 577ms 2.92% std::map::lower_bound (inline) 0 0% 58.17% 575ms 2.91% std::_Rb_tree::_M_get_node (inline) 0 0% 58.17% 560ms 2.84% std::map::find (inline) 26ms 0.13% 58.31% 557ms 2.82% AbstractCellPopulation::GetCellUsingLocationIndex 7ms 0.035% 58.34% 547ms 2.77% CellPropertyCollection::GetPropertiesType (inline) 0 0% 58.34% 544ms 2.76% std::_Rb_tree::_Alloc_node::operator() (inline) 5ms 0.025% 58.37% 522ms 2.65% Element::Element 11ms 0.056% 58.42% 515ms 2.61% MutableMesh::ReIndex 9ms 0.046% 58.47% 498ms 2.52% Cylindrical2dMesh::ReconstructCylindricalMesh 2ms 0.01% 58.48% 496ms 2.51% std::ostream::operator<< (inline) 62ms 0.31% 58.79% 493ms 2.50% std::ostream::_M_insert 8ms 0.041% 58.83% 472ms 2.39% Element::RegisterWithNodes (inline) 14ms 0.071% 58.90% 465ms 2.36% Node::AddElement 299ms 1.52% 60.42% 457ms 2.32% AbstractCellMutationState::AbstractCellMutationState 11ms 0.056% 60.48% 457ms 2.32% Cylindrical2dMesh::CorrectNonPeriodicMesh 2ms 0.01% 60.49% 449ms 2.28% AbstractCellProperty::IsSubType (inline) 126ms 0.64% 61.12% 417ms 2.11% __GI___libc_free 19ms 0.096% 61.22% 362ms 1.83% divconqrecurse 13ms 0.066% 61.29% 353ms 1.79% Node::RemoveElement 105ms 0.53% 61.82% 353ms 1.79% std::_Rb_tree::_M_erase 13ms 0.066% 61.88% 353ms 1.79% std::_Rb_tree::erase 0 0% 61.88% 352ms 1.78% std::set::erase (inline) 11ms 0.056% 61.94% 342ms 1.73% std::__new_allocator::deallocate (inline) 29ms 0.15% 62.09% 339ms 1.72% std::_Rb_tree::~_Rb_tree (inline) 87ms 0.44% 62.53% 338ms 1.71% mergehulls 0 0% 62.53% 338ms 1.71% std::allocator_traits::deallocate (inline) 33ms 0.17% 62.70% 333ms 1.69% Element::ResetIndex 127ms 0.64% 63.34% 332ms 1.68% std::_Rb_tree::_M_get_insert_unique_pos 2ms 0.01% 63.35% 331ms 1.68% std::_Vector_base::_M_allocate (inline) 3ms 0.015% 63.36% 328ms 1.66% NodeLocationWriter::Visit 325ms 1.65% 65.01% 325ms 1.65% std::type_info::name (inline) 165ms 0.84% 65.85% 323ms 1.64% __cxxabiv1::__si_class_type_info::__do_dyncast 2ms 0.01% 65.86% 322ms 1.63% AbstractCellPopulation::GetLocationIndexUsingCell 5ms 0.025% 65.88% 318ms 1.61% Cell::GetCellProliferativeType 13ms 0.066% 65.95% 314ms 1.59% Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries 0 0% 65.95% 306ms 1.55% std::set::~set (inline) 32ms 0.16% 66.11% 297ms 1.51% AbstractCellPopulation::Iterator::IsRealCell 0 0% 66.11% 295ms 1.50% std::_Rb_tree::_M_drop_node (inline) 3ms 0.015% 66.13% 294ms 1.49% LegacyCellProliferativeTypesWriter::VisitCell 0 0% 66.13% 293ms 1.48% AbstractCellPopulation::Iterator::operator++ (inline) 226ms 1.15% 67.27% 290ms 1.47% _int_free 33ms 0.17% 67.44% 284ms 1.44% std::num_put::_M_insert_float 266ms 1.35% 68.79% 267ms 1.35% std::vector::operator[] (inline) 0 0% 68.79% 265ms 1.34% std::_Rb_tree::_M_put_node (inline) 3ms 0.015% 68.80% 257ms 1.30% Cell::GetMutationState 16ms 0.081% 68.88% 257ms 1.30% std::_Rb_tree::_Rb_tree (partial-inline) 7ms 0.035% 68.92% 256ms 1.30% AbstractCellPopulation::IsCellAttachedToLocationIndex 7ms 0.035% 68.95% 256ms 1.30% std::vector::push_back (inline) 17ms 0.086% 69.04% 248ms 1.26% AbstractTetrahedralElement::CalculateJacobian 16ms 0.081% 69.12% 241ms 1.22% std::vector::_M_realloc_insert 74ms 0.38% 69.50% 239ms 1.21% ApcOneHitCellMutationState::ApcOneHitCellMutationState 0 0% 69.50% 233ms 1.18% std::set::set (inline) 5ms 0.025% 69.52% 230ms 1.17% AbstractCentreBasedCellPopulation::GetNodeCorrespondingToCell (inline) 1ms 0.0051% 69.53% 230ms 1.17% TetrahedralMesh::RefreshJacobianCachedData 4ms 0.02% 69.55% 225ms 1.14% AbstractCentreBasedCellPopulation::IsCellAssociatedWithADeletedLocation 5ms 0.025% 69.57% 221ms 1.12% alternateaxes 216ms 1.09% 70.67% 216ms 1.09% [libchaste_cell_based.so] 198ms 1.00% 71.67% 215ms 1.09% vertexmedian 15ms 0.076% 71.75% 213ms 1.08% std::_Rb_tree::_M_copy (inline) 2ms 0.01% 71.76% 208ms 1.05% std::__cxx11::collate::do_transform 42ms 0.21% 71.97% 207ms 1.05% BetaCateninOneHitCellMutationState::BetaCateninOneHitCellMutationState 0 0% 71.97% 206ms 1.04% OffLatticeSimulation::ApplyBoundaries 17ms 0.086% 72.06% 203ms 1.03% TetrahedralMesh::Clear 41ms 0.21% 72.26% 202ms 1.02% ApcTwoHitCellMutationState::ApcTwoHitCellMutationState 0 0% 72.26% 201ms 1.02% ___vsnprintf 0 0% 72.26% 201ms 1.02% __vsnprintf_internal (inline) 13ms 0.066% 72.33% 201ms 1.02% std::_Rb_tree::_M_erase_aux (inline) 16ms 0.081% 72.41% 200ms 1.01% AbstractTetrahedralElement::CalculateInverseJacobian 23ms 0.12% 72.53% 196ms 0.99% __printf_buffer 57ms 0.29% 72.82% 195ms 0.99% std::_Rb_tree::_M_clone_node (inline) 146ms 0.74% 73.56% 190ms 0.96% AbstractElement::GetNodeGlobalIndex 14ms 0.071% 73.63% 190ms 0.96% AbstractTetrahedralElement::RefreshJacobian 9ms 0.046% 73.67% 185ms 0.94% Element::MarkAsDeleted 134ms 0.68% 74.35% 181ms 0.92% malloc_consolidate 181ms 0.92% 75.27% 181ms 0.92% std::_Rb_tree_insert_and_rebalance 1ms 0.0051% 75.27% 180ms 0.91% MeshBasedCellPopulation::GetDampingConstant 1ms 0.0051% 75.28% 179ms 0.91% AbstractCentreBasedCellPopulation::GetDampingConstant 7ms 0.035% 75.31% 175ms 0.89% CellProliferativeTypesWriter::VisitCell 11ms 0.056% 75.37% 164ms 0.83% MeshBasedCellPopulationWithGhostNodes::CalculateForceBetweenGhostNodes 3ms 0.015% 75.39% 161ms 0.82% CellPropertyCollection::HasProperty 1ms 0.0051% 75.39% 161ms 0.82% __printf_fp_spec (inline) 5ms 0.025% 75.42% 160ms 0.81% __printf_fp_l_buffer 0 0% 75.42% 158ms 0.8% Cell::HasCellProperty (inline) 62ms 0.31% 75.73% 157ms 0.8% AbstractElement::GetNodeLocation 3ms 0.015% 75.74% 154ms 0.78% AbstractTetrahedralElement::AbstractTetrahedralElement 98ms 0.5% 76.24% 154ms 0.78% Cylindrical2dMesh::GetVectorFromAtoB 151ms 0.77% 77.01% 151ms 0.77% incircle 150ms 0.76% 77.77% 150ms 0.76% Node::GetIndex 94ms 0.48% 78.24% 149ms 0.76% std::_Rb_tree::equal_range (inline) 71ms 0.36% 78.60% 145ms 0.73% __printf_fp_buffer_1 139ms 0.7% 79.31% 139ms 0.7% std::vector::size (inline) 138ms 0.7% 80.01% 138ms 0.7% unlink_chunk 52ms 0.26% 80.27% 136ms 0.69% ApcTwoHitCellMutationState::~ApcTwoHitCellMutationState (inline) 9ms 0.046% 80.32% 133ms 0.67% non-virtual thunk to WntCellCycleModel::AdjustOdeParameters(double) 0 0% 80.32% 130ms 0.66% WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel 126ms 0.64% 80.95% 126ms 0.64% AbstractCellMutationState::~AbstractCellMutationState 3ms 0.015% 80.97% 124ms 0.63% MeshBasedCellPopulation::SpringsEnd (inline) 1ms 0.0051% 80.98% 122ms 0.62% boost::numeric::ublas::vector_assign (inline) 119ms 0.6% 81.58% 119ms 0.6% AbstractElement::IsDeleted 1ms 0.0051% 81.58% 118ms 0.6% AbstractCellBasedWriter::OpenOutputFileForAppend 0 0% 81.58% 118ms 0.6% CryptSimulationBoundaryCondition::ImposeBoundaryCondition 10ms 0.051% 81.63% 118ms 0.6% Node::~Node 49ms 0.25% 81.88% 118ms 0.6% std::__ostream_insert 39ms 0.2% 82.08% 117ms 0.59% ApcOneHitCellMutationState::~ApcOneHitCellMutationState (inline) 36ms 0.18% 82.26% 115ms 0.58% BetaCateninOneHitCellMutationState::~BetaCateninOneHitCellMutationState (inline) 30ms 0.15% 82.41% 115ms 0.58% TetrahedralMesh::EdgesEnd 1ms 0.0051% 82.42% 114ms 0.58% Cell::SetCellProliferativeType 0 0% 82.42% 112ms 0.57% OutputFileHandler::OpenOutputFile 4ms 0.02% 82.44% 112ms 0.57% boost::numeric::ublas::c_vector::c_vector (inline) 0 0% 82.44% 109ms 0.55% AbstractCellBasedSimulation::DoCellRemoval (inline) 103ms 0.52% 82.96% 109ms 0.55% vertexsort 1ms 0.0051% 82.97% 106ms 0.54% AbstractCellPopulation::OpenRoundRobinWritersFilesForAppend 106ms 0.54% 83.50% 106ms 0.54% TetrahedralMesh::EdgeIterator::operator!= 15ms 0.076% 83.58% 103ms 0.52% std::num_put::_M_insert_int 2ms 0.01% 83.59% 102ms 0.52% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 101ms 0.51% 84.10% 101ms 0.51% std::_Rb_tree_rebalance_for_erase 100ms 0.51% 84.61% 100ms 0.51% AbstractCellProperty::~AbstractCellProperty 27ms 0.14% 84.75% 99ms 0.5% boost::numeric::ublas::indexing_vector_assign